Hmm. What I am going to say maybe a little biased, but I will try to be as objective as possible. First of all, I have to say that I am a UERM student and I can give you my personal take on UERM. As you might know, we have a vertical type of PBL, which means that we study the normal people first. Meaning, our first year consists of an integration of Ana, Physio, Biochem, and Epi/Prev Med. Our 2nd and 3rd year consists on clinical modules which are organized by systems (i.e. Patho, Pharma, IM, Surg, Ob/gyn, Peds, etc.). I have to say that UERMs strength lies within their clinical training. Some say that we are weak in the basics (i.e. Ana, Physio, Biochem), but I personally think it is up to the student.
For instance, I like UERM because we get a lot of independent study time, which means we dont have too many classes and we can study on our own. This was especially helpful for me because I used this time to study for the USMLE. I was able to take the Step 1 exam between my 2nd and 3rd year and the Step 2 exam mid-way through my 3rd year. Another plus for UERM fil-am students is we are affiliated with a hospital in New York and we are aloud to take some of our rotations there. I personally will be doing IM, surgery, and Ob/Gyn, and Pediatrics in NY.
Lastly, I can personally attest that UERM has prepared me for the USMLE; I was able to get a 99/251 in Step 1 and a 98/242 in Step 2CK. Many of my fil-am classmates were able to pass and get high scores. Our school definitely has a passing rate higher than the ECFMG passing rate for IMGs. I know UST is a great school, their tradition and excellence cannot be disputed. UST has a higher Filipino board passing rate than UERM (at least since 1999). One thing to consider when coming to the Philippines for medical school is that we are all IMGs when we go back to the States. No matter were you go to school, program directors see you as an IMG. The one of main criteria for getting a residency is your USMLE score. Personally, our PBL system prepares you better for USMLE type questions and thinking more clinically. But I cant speak for UST since I am not a student there. Either way, its up to the student, you cant go wrong with both schools.